2019
A chromosome-scale assembly of the major African malaria vector Anopheles funestus
Ghurye J, Koren S, Small S, Redmond S, Howell P, Phillippy A, Besansky N. A chromosome-scale assembly of the major African malaria vector Anopheles funestus. GigaScience 2019, 8: giz063. PMID: 31157884, PMCID: PMC6545970, DOI: 10.1093/gigascience/giz063.Peer-Reviewed Original ResearchConceptsReference genomeHigh-quality reference genomeCurrent reference assemblyHaploid genome sizeMajor African malaria vector Anopheles funestusN50 scaffold sizeChromosome-scale assemblyReference genome assemblyN50 contig sizeChromosome-scale scaffoldsMalaria vector Anopheles funestusAfrican malaria vector Anopheles funestusMbp of sequenceSingle-molecule sequencingPrimary assemblyAnopheles funestusHi-C dataImportant disease vectorChromosome scaffoldingGenome sizeGenome assemblyContig sizeReference assemblyGenomic variationAssociation of phenotypic
2018
Improved reference genome of Aedes aegypti informs arbovirus vector control
Matthews BJ, Dudchenko O, Kingan SB, Koren S, Antoshechkin I, Crawford JE, Glassford WJ, Herre M, Redmond SN, Rose NH, Weedall GD, Wu Y, Batra SS, Brito-Sierra CA, Buckingham SD, Campbell CL, Chan S, Cox E, Evans BR, Fansiri T, Filipović I, Fontaine A, Gloria-Soria A, Hall R, Joardar VS, Jones AK, Kay RGG, Kodali VK, Lee J, Lycett GJ, Mitchell SN, Muehling J, Murphy MR, Omer AD, Partridge FA, Peluso P, Aiden AP, Ramasamy V, Rašić G, Roy S, Saavedra-Rodriguez K, Sharan S, Sharma A, Smith ML, Turner J, Weakley AM, Zhao Z, Akbari OS, Black WC, Cao H, Darby AC, Hill CA, Johnston JS, Murphy TD, Raikhel AS, Sattelle DB, Sharakhov IV, White BJ, Zhao L, Aiden EL, Mann RS, Lambrechts L, Powell JR, Sharakhova MV, Tu Z, Robertson HM, McBride CS, Hastie AR, Korlach J, Neafsey DE, Phillippy AM, Vosshall LB. Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 2018, 563: 501-507. PMID: 30429615, PMCID: PMC6421076, DOI: 10.1038/s41586-018-0692-z.Peer-Reviewed Original ResearchMeSH KeywordsAedesAnimalsArbovirus InfectionsArbovirusesDengue VirusDNA Copy Number VariationsFemaleGenetic VariationGenetics, PopulationGenome, InsectGenomicsGlutathione TransferaseInsect ControlInsecticide ResistanceMaleMolecular Sequence AnnotationMosquito VectorsMultigene FamilyPyrethrinsReference StandardsSex Determination ProcessesConceptsGenome assemblySex-determining M locusHigh-quality genome assemblyInsecticide resistancePopulation genomic analysesQuantitative trait lociGlutathione S-transferase geneEgg-laying sitesNew biological insightsDangerous viral pathogensCopy number variationsDengue vector competenceCytogenetic mapTrait lociReference genomeGenomic analysisBiological insightsDisease vectorsM locusFemale Aedes aegypti mosquitoesIonotropic receptorsVector competenceHuman hostAedes aegypti mosquitoesLoci
2017
Genetic diversity of the African malaria vector Anopheles gambiae
Miles A, Harding N, Bottà G, Clarkson C, Antão T, Kozak K, Schrider D, Kern A, Redmond S, Sharakhov I, Pearson R, Bergey C, Fontaine M, Donnelly M, Lawniczak M, Kwiatkowski D, Donnelly M, Ayala D, Besansky N, Burt A, Caputo B, della Torre A, Fontaine M, Godfray H, Hahn M, Kern A, Kwiatkowski D, Lawniczak M, Midega J, Neafsey D, O’Loughlin S, Pinto J, Riehle M, Sharakhov I, Vernick K, Weetman D, Wilding C, White B, Troco A, Pinto J, Diabaté A, O’Loughlin S, Burt A, Costantini C, Rohatgi K, Besansky N, Elissa N, Pinto J, Coulibaly B, Riehle M, Vernick K, Pinto J, Dinis J, Midega J, Mbogo C, Bejon P, Wilding C, Weetman D, Mawejje H, Donnelly M, Weetman D, Wilding C, Donnelly M, Stalker J, Rockett K, Drury E, Mead D, Jeffreys A, Hubbart C, Rowlands K, Isaacs A, Jyothi D, Malangone C, Vauterin P, Jeffery B, Wright I, Hart L, Kluczyński K, Cornelius V, MacInnis B, Henrichs C, Giacomantonio R, Kwiatkowski D. Genetic diversity of the African malaria vector Anopheles gambiae. Nature 2017, 552: 96-100. PMID: 29186111, PMCID: PMC6026373, DOI: 10.1038/nature24995.Peer-Reviewed Original Research
2016
Genomic Dark Matter Illuminated: Anopheles Y Chromosomes
Redmond S, Neafsey D. Genomic Dark Matter Illuminated: Anopheles Y Chromosomes. Trends In Parasitology 2016, 32: 585-587. PMID: 27263828, DOI: 10.1016/j.pt.2016.05.008.Commentaries, Editorials and Letters
2013
The zebrafish reference genome sequence and its relationship to the human genome
Howe K, Clark M, Torroja C, Torrance J, Berthelot C, Muffato M, Collins J, Humphray S, McLaren K, Matthews L, McLaren S, Sealy I, Caccamo M, Churcher C, Scott C, Barrett J, Koch R, Rauch G, White S, Chow W, Kilian B, Quintais L, Guerra-Assunção J, Zhou Y, Gu Y, Yen J, Vogel J, Eyre T, Redmond S, Banerjee R, Chi J, Fu B, Langley E, Maguire S, Laird G, Lloyd D, Kenyon E, Donaldson S, Sehra H, Almeida-King J, Loveland J, Trevanion S, Jones M, Quail M, Willey D, Hunt A, Burton J, Sims S, McLay K, Plumb B, Davis J, Clee C, Oliver K, Clark R, Riddle C, Elliott D, Threadgold G, Harden G, Ware D, Begum S, Mortimore B, Kerry G, Heath P, Phillimore B, Tracey A, Corby N, Dunn M, Johnson C, Wood J, Clark S, Pelan S, Griffiths G, Smith M, Glithero R, Howden P, Barker N, Lloyd C, Stevens C, Harley J, Holt K, Panagiotidis G, Lovell J, Beasley H, Henderson C, Gordon D, Auger K, Wright D, Collins J, Raisen C, Dyer L, Leung K, Robertson L, Ambridge K, Leongamornlert D, McGuire S, Gilderthorp R, Griffiths C, Manthravadi D, Nichol S, Barker G, Whitehead S, Kay M, Brown J, Murnane C, Gray E, Humphries M, Sycamore N, Barker D, Saunders D, Wallis J, Babbage A, Hammond S, Mashreghi-Mohammadi M, Barr L, Martin S, Wray P, Ellington A, Matthews N, Ellwood M, Woodmansey R, Clark G, Cooper J, Tromans A, Grafham D, Skuce C, Pandian R, Andrews R, Harrison E, Kimberley A, Garnett J, Fosker N, Hall R, Garner P, Kelly D, Bird C, Palmer S, Gehring I, Berger A, Dooley C, Ersan-Ürün Z, Eser C, Geiger H, Geisler M, Karotki L, Kirn A, Konantz J, Konantz M, Oberländer M, Rudolph-Geiger S, Teucke M, Lanz C, Raddatz G, Osoegawa K, Zhu B, Rapp A, Widaa S, Langford C, Yang F, Schuster S, Carter N, Harrow J, Ning Z, Herrero J, Searle S, Enright A, Geisler R, Plasterk R, Lee C, Westerfield M, de Jong P, Zon L, Postlethwait J, Nüsslein-Volhard C, Hubbard T, Crollius H, Rogers J, Stemple D. The zebrafish reference genome sequence and its relationship to the human genome. Nature 2013, 496: 498-503. PMID: 23594743, PMCID: PMC3703927, DOI: 10.1038/nature12111.Peer-Reviewed Original ResearchConceptsHigh-quality sequence assembliesHuman protein-coding genesProtein-coding genesReference genome sequenceKey genomic featuresHuman reference genomeZebrafish genomeZebrafish orthologueReference genomeGenome sequenceHuman genomeSequence assemblyGenomic featuresLarge genesGenomeGenesOrthologuesVertebratesSequenceAssembly
2012
Transcriptome of the adult female malaria mosquito vector Anopheles albimanus
Martínez-Barnetche J, Gómez-Barreto R, Ovilla-Muñoz M, Téllez-Sosa J, López D, Dinglasan R, Mohien C, MacCallum R, Redmond S, Gibbons J, Rokas A, Machado C, Cazares-Raga F, González-Cerón L, Hernández-Martínez S, López M. Transcriptome of the adult female malaria mosquito vector Anopheles albimanus. BMC Genomics 2012, 13: 207. PMID: 22646700, PMCID: PMC3442982, DOI: 10.1186/1471-2164-13-207.Peer-Reviewed Original ResearchConceptsMalaria vectorsProtein-coding transcriptsAvailable genomic informationPlasmodium-mosquito interactionsHigh-quality assemblyImportant malaria vectorAnopheles albimanusFemale transcriptomesPutative orthologsDivergence timesPlasmodium lifecycleEukaryotic genomesTranscriptome projectsEvolutionary biologyInterPro annotationProtein familyMosquito biologyInsect vectorsGenomic informationNeotropical vectorsCDNA libraryIllumina sequencesAnopheline mosquito vectorsGenus AnophelesFat body
2010
SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes
Neafsey D, Lawniczak M, Park D, Redmond S, Coulibaly M, Traoré S, Sagnon N, Costantini C, Johnson C, Wiegand R, Collins F, Lander E, Wirth D, Kafatos F, Besansky N, Christophides G, Muskavitch M. SNP Genotyping Defines Complex Gene-Flow Boundaries Among African Malaria Vector Mosquitoes. Science 2010, 330: 514-517. PMID: 20966254, PMCID: PMC4811326, DOI: 10.1126/science.1193036.Peer-Reviewed Original ResearchConceptsGenomic differentiationGenome-wide monitoringGreater genetic divergenceVector mosquito populationsMalaria vector mosquitoesAfrican malaria vector mosquitoesReproductive isolationBehavioral diversificationGenetic divergenceGenomic regionsNatural selectionPopulation structurePolymorphic inversionsSelective eventsSNP genotypingVector control effortsMosquito populationsVector mosquitoesDifferentiationComplex showDivergenceMosquitoesCentromeresGenomeSpeciesWidespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences
Lawniczak M, Emrich S, Holloway A, Regier A, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang S, Minx P, Nelson J, Kyung K, Walenz B, Garcia-Hernandez E, Aguiar M, Viswanathan L, Rogers Y, Strausberg R, Saski C, Lawson D, Collins F, Kafatos F, Christophides G, Clifton S, Kirkness E, Besansky N. Widespread Divergence Between Incipient Anopheles gambiae Species Revealed by Whole Genome Sequences. Science 2010, 330: 512-514. PMID: 20966253, PMCID: PMC3674514, DOI: 10.1126/science.1195755.Peer-Reviewed Original ResearchConceptsSpeciation processGenome sequencePrevious genome-wide scanHeterogeneous genomic divergenceAnopheles gambiae speciesGenome-wide scanUnknown genetic mechanismsWhole genome sequencesGene flowGenomic divergenceLarval ecologyGambiae speciesAnopheles gambiae sensu strictoPericentromeric regionGambiae sensu strictoGenetic mechanismsWidespread divergenceSensu strictoReproductive behaviorMajor vectorDivergenceSpeciationSequenceAppreciable levelsMolecular forms